Variant report

Variant	rs7575170
Chromosome Location	chr2:55886780-55886781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55884125..55886913-chr2:55887602..55890288,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10207590	0.81[ASN][1000 genomes]
rs12329050	0.80[EUR][1000 genomes]
rs12473585	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12473621	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12617627	0.85[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.96[YRI][hapmap]
rs12617719	0.83[ASN][1000 genomes]
rs12618859	0.85[ASW][hapmap];0.96[YRI][hapmap]
rs12619903	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12986587	0.80[JPT][hapmap]
rs12992408	0.83[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs12992827	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12993624	0.85[ASW][hapmap];0.88[YRI][hapmap]
rs12999966	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13001425	0.85[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13002860	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007577	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13009239	0.82[ASN][1000 genomes]
rs13009447	0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13009906	0.93[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.92[YRI][hapmap]
rs13010217	0.85[ASW][hapmap];0.96[YRI][hapmap]
rs13013133	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13013699	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13014898	0.82[CHB][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs13015018	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13015030	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs13021958	0.90[YRI][hapmap]
rs13025331	0.85[ASW][hapmap];0.96[YRI][hapmap]
rs13032503	0.93[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.92[YRI][hapmap]
rs1318672	0.86[CHB][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap]
rs1443746	0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs17800203	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1822513	0.85[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34513671	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34679603	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3791654	0.92[YRI][hapmap]
rs4322879	0.96[YRI][hapmap]
rs5012561	0.81[CEU][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs56122729	0.87[ASN][1000 genomes]
rs6737995	0.85[ASW][hapmap];0.96[YRI][hapmap]
rs6757006	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs7592219	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596377	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8080	0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7575170	PNPT1	cis	cerebellum	SCAN
rs7575170	CCDC104	cis	parietal	SCAN
rs7575170	SMEK2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
4	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
5	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:55864400-55919600	Weak transcription	NHLF	lung
7	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
10	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
12	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
14	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:55870800-55903600	Weak transcription	Gastric	stomach
16	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
18	chr2:55871000-55887800	Weak transcription	Esophagus	oesophagus
19	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
21	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
22	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
24	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
25	chr2:55873000-55888400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:55873200-55893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
28	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
30	chr2:55875600-55887200	Weak transcription	K562	blood
31	chr2:55879000-55888800	Strong transcription	Liver	Liver
32	chr2:55879000-55889000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:55879000-55890400	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:55879000-55891800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:55879000-55896200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:55879200-55889800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:55879200-55902800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:55879400-55914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:55879600-55891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:55880000-55887800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:55880400-55889600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:55880400-55890800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:55881200-55913000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:55881800-55887800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:55881800-55898000	Weak transcription	NHDF-Ad	bronchial
47	chr2:55882000-55887600	Weak transcription	Lung	lung
48	chr2:55882000-55887800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:55882000-55893400	Weak transcription	Right Ventricle	heart
50	chr2:55882000-55893400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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